def wf_bandstructure_hse(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
wf_src_name = "bandstructure_hse_full.yaml"
wf = get_wf(structure,
wf_src_name,
vis=MPHSERelaxSet(structure, force_gamma=True),
common_params={
"vasp_cmd": vasp_cmd,
"db_file": db_file
})
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf,
fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_bandstructure_plus_boltztrap(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
params = []
for x in range(4):
params.append({"vasp_cmd": vasp_cmd, "db_file": db_file})
params.append({"db_file": db_file})
wf = get_wf(structure, "bandstructure_boltztrap.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
params=params)
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf, fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_bandstructure_plus_boltztrap(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
params = []
for x in range(4): # everything but BoltzTrap task
params.append({"vasp_cmd": vasp_cmd, "db_file": db_file})
params.append({"db_file": db_file})
wf = get_wf(structure,
"bandstructure_boltztrap.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
params=params)
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf,
fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_bandstructure_plus_hse(structure, gap_only=True, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
if gap_only:
wf_src_name = "bandstructure_hsegap.yaml"
else:
wf_src_name = "bandstructure_hse.yaml"
wf = get_wf(structure, wf_src_name,
vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": vasp_cmd,
"db_file": db_file})
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf, fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_bandstructure2D(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
vdw_kernel = c.get("VDW_KERNEL_DIR", VDW_KERNEL_DIR)
incar = _read_user_incar('Relax2D.txt')
print(incar)
mpr2d = MPRelaxSet(structure, force_gamma=True, user_incar_settings=incar)
mpr2dstatic = MPRelaxSet(structure,
force_gamma=True,
user_incar_settings={
"NEDOS": "3001",
"EMIN": "-15.0",
"EMAX": "15.0"
})
#fws = [OptimizeFW2D(structure=structure, vasp_input_set=mpr2d, vasp_cmd=vasp_cmd, db_file=db_file, vdw_kernel_dir=vdw_kernel)]
fws = [
OptimizeFW2D(structure=structure,
vasp_input_set=mpr2d,
vasp_cmd=vasp_cmd,
vdw_kernel_dir=vdw_kernel)
]
fws.append(StaticFW2D(parents=fws[0], vasp_input_set=mpr2dstatic))
#fws.append(NonSCFFW2D(parents=fws[1], mode='uniform'))
fws.append(NonSCFFW2D(parents=fws[1], mode='line'))
wf = Workflow(fws)
'''check bandstructure.yaml'''
'''
wf = get_wf(structure, "bandstructure.yaml", vis=MPScanRelaxSet2D(structure, force_gamma=True,), \
params=[{'vasp_input_set': mpr2d},{},{},{}], common_params={"vasp_cmd": vasp_cmd, "db_file": db_file,}) #"vdw_kernel_dir": vdw_kernel})
'''
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf,
fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
wf.name = "{}:{}".format(structure.composition.reduced_formula,
"bandStructure")
'''
fws = wf.fws
fws[0] = new_firework
print(fws)
'''
return wf
def get_wf(self, c=None):
"""
Get the workflow.
Returns:
Workflow
"""
c = c or {"VASP_CMD": VASP_CMD, "DB_FILE": DB_FILE}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
nsites = len(self.structure.sites)
vis = MPRelaxSet(self.structure, potcar_functional="PBE_54", force_gamma=True)
opt_fw = OptimizeFW(
self.structure,
vasp_input_set=vis,
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
)
vis = MPStaticSet(self.structure, potcar_functional="PBE_54", force_gamma=True)
static_fw = StaticFW(
self.structure,
vasp_input_set=vis,
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
parents=[opt_fw],
)
# Separate FW for each BZ surface calc
# Run Z2Pack on unique TRIM planes in the BZ
surfaces = ["kx_0", "kx_1"]
equiv_planes = self.get_equiv_planes()
# Only run calcs on inequivalent BZ surfaces
if self.symmetry_reduction:
for add_surface in equiv_planes.keys():
mark = True
for surface in surfaces:
if surface in equiv_planes[add_surface]:
mark = False
if mark and add_surface not in surfaces:
surfaces.append(add_surface)
else: # 4 TRI surfaces define Z2 in 3D
surfaces = ["kx_1", "ky_1", "kz_0", "kz_1"]
z2pack_fws = []
for surface in surfaces:
z2pack_fw = Z2PackFW(
parents=[static_fw],
structure=self.structure,
surface=surface,
uuid=self.uuid,
name="z2pack",
vasp_cmd=c["VASP_CMD"],
db_file=c["DB_FILE"],
)
z2pack_fws.append(z2pack_fw)
analysis_fw = InvariantFW(
parents=z2pack_fws,
structure=self.structure,
symmetry_reduction=self.symmetry_reduction,
equiv_planes=equiv_planes,
uuid=self.uuid,
name="invariant",
db_file=c["DB_FILE"],
)
fws = [opt_fw, static_fw] + z2pack_fws + [analysis_fw]
wf = Workflow(fws)
wf = add_additional_fields_to_taskdocs(wf, {"wf_meta": self.wf_meta})
# Add vdW corrections if structure is layered
dim_data = StructureDimensionality(self.structure)
if np.any(
[
dim == 2
for dim in [dim_data.larsen_dim, dim_data.cheon_dim, dim_data.gorai_dim]
]
):
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {
"IVDW": 11,
"EDIFFG": 0.005,
"IBRION": 2,
"NSW": 100,
}
},
fw_name_constraint="structure optimization",
)
wf = add_modify_incar(
wf,
modify_incar_params={"incar_update": {"IVDW": 11}},
fw_name_constraint="static",
)
wf = add_modify_incar(
wf,
modify_incar_params={"incar_update": {"IVDW": 11}},
fw_name_constraint="z2pack",
)
else:
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"EDIFFG": 0.005, "IBRION": 2, "NSW": 100}
},
fw_name_constraint="structure optimization",
)
# Helpful vasp settings and no parallelization
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {
"ADDGRID": ".TRUE.",
"LASPH": ".TRUE.",
"GGA": "PS",
"NCORE": 1,
}
},
)
# Generate inputs for Z2Pack with a static calc
wf = add_modify_incar(
wf,
modify_incar_params={"incar_update": {"PREC": "Accurate"}},
fw_name_constraint="static",
)
wf = add_common_powerups(wf, c)
wf.name = "{} {}".format(self.structure.composition.reduced_formula, "Z2Pack")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf, fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, self.structure)
tag = "z2pack: {}".format(self.uuid)
wf = add_tags(wf, [tag])
return wf
def wf_irvsp(structure, magnetic=False, soc=False, v2t=False, c=None):
"""
Fireworks workflow for running an irvsp calculation.
Optionally performs a vasp2trace calculation.
Args:
structure (Structure): Pymatgen structure object
magnetic (bool): Whether the calculation is on a magnetic structure
soc (bool): Spin-orbit coupling included
v2t (bool): Do a vasp2trace calculation in addition to irvsp.
Returns:
Workflow
"""
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
uuid = str(uuid4())
wf_meta = {"wf_uuid": uuid, "wf_name": "Irvsp WF"}
magmoms = None
if magnetic and "magmom" in structure.site_properties:
magmoms_orig = structure.site_properties["magmom"]
magmoms = [str(m) for m in magmoms_orig]
magmoms = " ".join(magmoms)
elif magnetic:
raise RuntimeError(
"Structure must have magnetic moments in site_properties for magnetic calcualtion!"
)
ncoords = 3 * len(structure.sites)
nbands = 0
for site in structure.sites:
nbands += site.species.total_electrons
trim_kpoints = Kpoints(
comment="TRIM Points",
num_kpts=8,
style=Kpoints.supported_modes.Reciprocal,
kpts=(
(0, 0, 0),
(0.5, 0, 0),
(0, 0.5, 0),
(0, 0, 0.5),
(0.5, 0.5, 0),
(0, 0.5, 0.5),
(0.5, 0, 0.5),
(0.5, 0.5, 0.5),
),
kpts_shift=(0, 0, 0),
kpts_weights=[1, 1, 1, 1, 1, 1, 1, 1],
coord_type="Reciprocal",
labels=["gamma", "x", "y", "z", "s", "t", "u", "r"],
tet_number=0,
tet_weight=0,
tet_connections=None,
)
# params dicts for wf
params = [
{}, # optimization
{}, # standardization
{}, # static
{
"input_set_overrides": {
"other_params": {"user_kpoints_settings": trim_kpoints}
}
}, # nscf
{"wf_uuid": uuid}, # irvsp
]
if magnetic and v2t:
yaml_spec = "irvsp_v2t_magnetic.yaml"
params.append({})
elif v2t:
yaml_spec = "irvsp_v2t.yaml"
params.append({})
else:
yaml_spec = "irvsp.yaml"
wf = get_wf(
structure,
yaml_spec,
params=params,
vis=MPStaticSet(structure, potcar_functional="PBE_54", force_gamma=True),
common_params={"vasp_cmd": vasp_cmd, "db_file": db_file},
wf_metadata=wf_meta,
)
dim_data = StructureDimensionality(structure)
if np.any(
[
dim == 2
for dim in [dim_data.larsen_dim, dim_data.cheon_dim, dim_data.gorai_dim]
]
):
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"IVDW": 11, "EDIFFG": 0.005, "IBRION": 2, "NSW": 100}
},
fw_name_constraint="structure optimization",
)
else:
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"EDIFFG": 0.005, "IBRION": 2, "NSW": 100}
},
fw_name_constraint="structure optimization",
)
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"ADDGRID": ".TRUE.", "LASPH": ".TRUE.", "GGA": "PS"}
},
)
# Includ ncl magmoms with saxis = (0, 0, 1)
if magnetic and soc:
magmoms = []
for m in magmoms_orig:
magmoms += [0.0, 0.0, m]
magmoms = [str(m) for m in magmoms]
magmoms = " ".join(magmoms)
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"ISYM": 2, "MAGMOM": "%s" % magmoms}
},
)
if magnetic and not soc:
# Include magmoms in every calculation
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"ISYM": 2, "MAGMOM": "%s" % magmoms, "ISPIN": 2}
},
)
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {
"ISYM": 2,
"LSORBIT": ".TRUE." if soc else ".FALSE.",
"MAGMOM": "%s" % magmoms
if magnetic
else "%i*0.0" % ncoords,
"ISPIN": 2 if magnetic and not soc else 1,
"LWAVE": ".TRUE.",
# "NBANDS": nbands,
}
},
fw_name_constraint="nscf",
)
wf = add_common_powerups(wf, c)
wf = add_additional_fields_to_taskdocs(wf, {"wf_meta": wf_meta},
task_name_constraint="VaspToDb")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf, fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_vasp2trace_magnetic(structure, c=None):
"""
Fireworks workflow for running a vasp2trace calculation
on a magnetic material.
Args:
structure (Structure): Pymatgen structure object with
magmom site property.
Returns:
Workflow
"""
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
ncoords = 3 * len(structure.sites)
if "magmom" in structure.site_properties:
magmoms = structure.site_properties["magmom"]
magmoms = [str(m) for m in magmoms]
magmoms = " ".join(magmoms)
nbands = 0
for site in structure.sites:
nbands += site.species.total_electrons
trim_kpoints = Kpoints(
comment="TRIM Points",
num_kpts=8,
style=Kpoints.supported_modes.Reciprocal,
kpts=(
(0, 0, 0),
(0.5, 0, 0),
(0, 0.5, 0),
(0, 0, 0.5),
(0.5, 0.5, 0),
(0, 0.5, 0.5),
(0.5, 0, 0.5),
(0.5, 0.5, 0.5),
),
kpts_shift=(0, 0, 0),
kpts_weights=[1, 1, 1, 1, 1, 1, 1, 1],
coord_type="Reciprocal",
labels=["gamma", "x", "y", "z", "s", "t", "u", "r"],
tet_number=0,
tet_weight=0,
tet_connections=None,
)
wf_path = os.path.join(os.path.dirname(__file__), "vasp2trace_magnetic.yaml")
wf = get_wf(
structure,
wf_path,
params=[
{},
{},
{
"input_set_overrides": {
"other_params": {"user_kpoints_settings": trim_kpoints}
}
},
{},
],
vis=MPStaticSet(structure, potcar_functional="PBE_54", force_gamma=True),
common_params={"vasp_cmd": vasp_cmd, "db_file": db_file},
)
dim_data = StructureDimensionality(structure)
if np.any(
[
dim == 2
for dim in [dim_data.larsen_dim, dim_data.cheon_dim, dim_data.gorai_dim]
]
):
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"IVDW": 11, "EDIFFG": 0.005, "IBRION": 2, "NSW": 100}
},
fw_name_constraint="structure optimization",
)
else:
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"EDIFFG": 0.005, "IBRION": 2, "NSW": 100}
},
fw_name_constraint="structure optimization",
)
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"ADDGRID": ".TRUE.", "LASPH": ".TRUE.", "GGA": "PS"}
},
)
# Include magmoms in every calculation
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {"ISYM": 2, "MAGMOM": "%s" % magmoms, "ISPIN": 2}
},
)
# Spin-polarized band structure
wf = add_modify_incar(
wf,
modify_incar_params={
"incar_update": {
"ISYM": 2,
"LSORBIT": ".FALSE.",
"MAGMOM": "%s" % magmoms,
"ISPIN": 2,
"LWAVE": ".TRUE.",
"NBANDS": nbands,
}
},
fw_name_constraint="nscf",
)
wf = add_common_powerups(wf, c)
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf, fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
